Left Broken
by Enailif
Summary: The past finally caught up to Skipper. The penguins must face their new lives when Skipper is needed on secret missions, one day not coming back. He left them clues, knowing that they will be the only ones to finish what he has started. But the team is tore apart. And Private will not stop searching. Meanwhile Marlene finds out that all the secrets have been lying in the zoo...
1. Chapter 1 The Homeleaving

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 **Left Broken**

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 **Chapter 1**

 **The Homeleaving**

"We are leaving the zoo"

Everything has been usual, king Julien having his crazy parties that no one wanted to join, Skipper yelling at him to turn of the loud music, Alice bringing food to animals with emotionless face showing how dissatisfied she was with her work, gorillas eating bananas and throwing them away to random places, monkeys playing chess. It has always been like that until the day those words were said by the penguin leader.

"We are leaving the zoo" Skipper stated as if it was nothing special, as if this meant nothing to their lifes.

"We WHAT?!" Kowalski gasped spatting out the coffee he had just drunk.

"Exactly what I had said. We are leaving"

"But sir, What happened? Why now?"

"There's not much to talk about. I will explain you on the way. Pack your things"

"What's up?" Private, who had heard them talking, came in and looked at the two penguins.

"Skipper decided that we are leaving the zoo like right now" Kowalski replied.

"You can't be serious"

"I am your leader, you must obey" Skipper told them and turned toward ladder to leave HQ, leaving his comrades in shock.

"What has gotten into him?"

"I have no idea, but he was serious. It doesn't seem to be a decision made under the influence of random emotions" Kowalski said.

"I think I should talk to him" Private decided to draw Skipper away from the fatal idea. He waddled to climb out of the headquarter and got onto the platform of their habitat. He found his leader standing on the edge of it, looking up at the sky slowly getting dark with late sunset.

"Skippah, are you sure about that? Do you want us to completely change our lives just on a command? We have friends, we have spent our best time here and now we are supposed to leave our memories behind?"

"Young Private, you have to recon with hard decisions that appear in every soldier's life. I got used to it. Instantly changing personalities, leaving the undone past behind, forgetting the memories because there's no place for them. One day you will be old enough to understand it all" The leader penguin spoke, patting Private on his back.

"But we are not like you, it's something new for us, we have never faced such a hard decision…"

"This day had to come, sooner or later" Skipper simply said, he didn't look like he would miss the central park zoo nor its inhabitants "We are leaving this night. You have time to say goodbyes"

"Can you tell us at least where are we going?"

"Classified"

With that Private resigned from asking more questions, it was pointless and nothing would make Skipper change his plans. He returned to share the information he got with Kowalski and Rico. They were waiting for him, hoping he would bring some good news. Their smiles fell when they saw his sad expression. The young penguin lowered his head and shook it.

"We only have time to say goodbye to everybody" He told his teammates.

"So this is the end? Farewell?"

"Ahw, I don't likea fare wells" Rico babbled, his voice unhappy.

"Neither do I" Kowalski joined and sighed "We should go visit our friends for the last time"

Meanwhile Skipper went to an otter habitat. If anyone should tell Marlene about their leaving it should be him. His teammates would not make her understand. Well, probably even he would not be able to make her understand since he wasn't sure himself about it. What he was doing was the best for everyone but he had to admit, the hardest moths of his life were awaiting him. The past was catching up to him. Oh dear. He stood at the mouth of a cave and knocked, waiting for his friend to show up. A while later chestnut-fur otter came out greeting him with a smile.

"Hey Skipper, What's up?" She said cheerfully.

"There's something important I need to tell you. Please try to not get me wrong" He told and saw her face change serious. Then he continued "Me and my team are moving out this night"

"Did I really hear what I heard?" She said after she had analyzed his words.

"I know it's hard, Marlene, this is the last time we see each other"

"But yesterday everything was fine, we played cards, remember? What has gotten into you!"

"Situation has changed"

"No, no, no, do not tell me such things. You are not going anywhere" Marlene said, her voice assertive.

"I hoped you would understand…"

"What's there to understand? What has changed since yesterday!?" She flustrated.

"Classified"

"Oh sure, classified, what else should I have expected in reply from you. You know what? This is just selfish!"

"Trust me, I'm doing what's the best for all of us"

"A greater good huh? I don't believe you. You got bored of us, we and the zoo are not as entertaining as you super secret life. Then fine, have your exciting life back, full of spies, missions, sudden explosions and this stuff. You won't even tell me the truth which I deserve to know. This only means we have never really been best friends"

"The truth is dangerous for you"

"Fine" she just said trying to hold back her emotions shutting her eyes, tears coming.

"Marlene…" Skipper said putting his flipper on her shoulder but she shook it off.

"If this is goodbye then I don't want it" with that the otter turned and walked away to disappear in her cave, not even bothering to look back.

"I am sorry" The leader penguin said quietly and waddled away.

The three penguins made a round around the zoo to visit every inhabitants. Farewell is never easy. It is never easy to fortget. And even harder to accept. The fate decided to mess up with their lives and they had to put on a mask and pretend that everything was fine. It was what Skipper always did. After the monkeys, Phil and Mason, it was time for the lemurs. They made their way to the habitat and saw Julien dancing near his royal throne followed by Maurice and Mort.

"Guys, can we please talk?"

"What makes you think I would talk to a silly penguin?" Julien said with his pride, as usual.

"Sure" Maurice agreed seeing that situation was serious. He turned off a boombox meeting his king's dissatisfied look.

"Well, we came to say goodbye. We are moving out"

"Oh, that's.." Maurice started trying to find good words. He kinda liked the penguins although they sometimes were annoying him "I haven't expected that"

"None of us did"

"Oh, so the silly penguins are going on a vacation?" Julien, of course, didn't get what they meant by 'moving out' "Bring me a souvenir. It doesn't have to be big. It just have to be shining and expensive"

"Eh, I'm gonna miss his misunderstood-ness" Kowalski thought.

"No penguins in the zoo?" Mort asked hugging Private's foot with tearful eyes.

"Yes Mort" The young penguin answered sadly. Just then their leader showed up.

"Are you ready boys?"

"Remember to bring me something shiny from your vacation!" Julien reminded him.

"Ummm, sure. I am definitely not going to miss you, ringtail"

"Neither do I!" The lemur said resentful and grabbed his furry tail.

"I will take care of your home" Mort stated still hugging Private's foot.

"Don't worry sad eyes" Skipper patted the little lemur "Goodbye Maurice"

They saluted and left, walking through the zoo alley. Probably for the last time in their lives. They weren't ready for that, it's never easy. Skipper's past were classified but he surely got used to it, he didn't feel like they did. Maybe he never did? He wasn't kind of a sentimental person, He might have been created for the life like that. But they did not.

Especially Private, he has always been the one to make friends quickly, maybe he was naïve but he saw the good in everybody. He knew that he would never forgive himself that there was a day when he just said goodbye and turned away from his peaceful life. Maybe Skipper for hunting for new adventures? They had some missions in the zoo but they might not be enough for the leader. There were so many possibilities of what has pulled him into making this decision but Private wanted to hear the reason from Skipper. He demanded it.

The penguins got to the headquarter to destroy any evidence of residency. They had to destroy everything, nothing could be left. Kowalski covered his eyes with his flippers as Skipper let Rico blow up all of his inventions. They took only the necessary things. Even the box of Skipper's logs, the only hint of what he was doing in past got burned by a flamethrower. At least Rico had fun.

"Sir, we haven't been to Marlene's yet" Kowalski spoke.

"No time for that"

"But Skippah, she's our best friend! We must…" Private started but he was cut off by his leader.

"You must obey my order"

"She needs to know"

"She has been informed already"

"But we want to see her"

"Private, believe me, she's not in the best mood to see you" Skipper sighed.

"What did you told her?"

"I just let her know that we are leaving, that's all"

"She was our best friend. Do you order us to leave her like that?"

"She doesn't want any goodbyes. She will accept it, just needs time. Like you boys"

"Poor Marlene, she must fell so lonely…" Kowalski said. But there was no point in continuing on that conversation. The moment they passed through the zoo gate was the moment they left the past behind, stepping into new chapter of their life.

They just followed Skipper with no clue where he was leading them. The passed through dark central park and reached the town. Their leader led them to subway, carefully to not get noticed by humans. They waited for it to arrive and quickly slipped into it, fortunately there were so many people that they couldn't be noticed through the crowd. They took their places on the floor under the seats.

"So, will you finally tell us where are we going?" Kowalski asked.

"Can't you just wait?" Skipper sighed.

"No" Private demanded.

"Okay. We are going to MAAB, a shortcut of Main America Agents Base. The base I used to work for in the past. I got information that I am needed there. It seems they have a problem, an enemy that I dealt with long time ago. They have a mission for me and I can't reject. I have to end what I have started, otherwise we all will be in danger. We had to leave the zoo, you will understand"

"Who is the enemy?"

"Classified"

"So, what mission?"

"Classified"

"Oh Skipper come on" Kowalski pleaded.

"What will happen to us?" Private asked.

"You are soon to find out. Welcome to your new lives boys"

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 **Please read.**

 **Well, PoM is not my main focus anymore, I decided to put all my stories on hiatus because I am writing for other fanbase now. But recently I watched the PoM movie and all the memories of the penguins I love came back to me. I thought it would be a right thing to do to write my last fanfic for them. This is just an idea I got a long time and decided to put it into a story. So I wrote this but I don't know if I should continue. It depends on you guys, so please, leave me a review. I would be grateful.**


	2. Chapter 2 Plans Have Changed

**Chapter 2**

 **Plans Have Changed**

The three penguins were tired by the journey, they were in the subway for who knows how long, then moved to a bus, hoping that Skipper knew what he was doing. Very few hours of sleep didn't make them feel better while their leader didn't show any sign of tiredness. Finally he got up and waddled to exit the mean of transport, his team followed.

"Where are we, sir?" Kowalski asked looking around, it was a city, unknown to him.

"Killen"

"Is it our destination? I hope so" Private said as he leaned on Rico for support, slowly falling asleep.

"It is. The biggest agents' base is lying in this town" Skipper said and admired the view "Hasn't been here in a while"

He gestured them to follow and slipped through the crowded pavements of Killen. They found suburbs and reached an old building, it looked abandoned. Skipper looked around to make sure no one was there, then he opened the door and they came in. It was dark, the penguins could barely see anything, so Rico spat out a flashlight, handing it to Skipper. Their leader went down the stairs leading to a basement and searched for something.

"Here it is" He spoke as he found a crate and pulled it "This is a tunnel"

"But Skippah, are we supposed to jump? I mean, it is a tunnel, but vertically down" Private feared.

"Trust me" Skipper told "Kowalski, you go first"

"Why me?"

"You are the oldest one of them"

"Umm, okay" Kowalski agreed looking at the tunnel hesitating. If there wasn't anything like a soft mattress downstairs then he was going to get smashed on the ground. Before he could make a decision something pushed him and he had no choice but to jump. He soon realized that it was Rico.

"Your turn Private" Skipper told the young penguin who gulped as he heard his teammates screams. "Come on"

"S-sure" Private tried not to show his fear as he looked down, he couldn't see the end, it seemed it was a long way down. Oh well, better to get it over with.

He closed his eyes and jumped. He thought he would scream like his teammates did, however no sound made it through his throat. The tunnel was slowly transforming into some kind a slide, he had to admit, it was fun. After several minutes he slowed down and reached the end. Before him was only a lift so he went ahead and stepped into it. The lift took him down but when it opened he was greeted by many rifles aimed at him. He did not expect that. Nor Skipper, probably. Private rose his flippers and saw Kowalski and Rico held by two of the security guards. Fortunately Skipper has appeared and pulled Private behind his back, aiming a gun at the agents. The young penguin didn't know that Skipper had one and brought it with him. Did he expect any dangers on their way?

"What is going on?" Skipper asked. Then from the crowd emerged a flat headed penguin, his eyebrows blonde. Buck Rockgut, He aimed his gun at him too "Don't you recognize me?"

"What did I tell you once when you came to my office? About the thing lying on my desk?"

"What? What is this all about?!"

"Answer me now!" Buck warned and prepared to pull the trigger.

"Your own secret invention. It was a robotic attachment to a flipper which could be used as a gun and was shining when enemies were near. You told me this in an act of your trust for me" Skipper quickly replied knowing that Rockgut would not hesitate to shoot.

"That's a good answer. Good to see you, friend" Buck said and they shook flippers giving each other brotherly pat on a shoulder. The agents lowered their weapon and released Kowalski with Rico. "I'm sorry for all of that. We found a spy in our headquarters, so the enemy knew about your arrival. I had to make sure. Someone could pretend to be you"

"We have much to discuss about" Skipper stated and looked at his team "They are exhausted"

"Don't worry. My people will show them to their room"

"Alright boys, go take a rest, tomorrow will be a hard day" He told the three penguins and went after Buck, while the agents ordered them to follow.

Kowalski was looking around the base with amazement. He was a scientist, it was understandable. The place was modern and huge, they were passing corridors looking into some rooms filled with high technology. Labs, computers, machines, special rooms for experiments with anti-vibration walls which Rico admired with 'kaboom' look in his eyes. They went upstairs, it was a floor for rooms in which the workers were living. One was reserved for them.

"You mustn't touch anything, don't leave the room" One of the agents told them and they were left alone. The room wasn't big, but it at least had comfortable triple-bed. There were no windows since they were under the ground. The penguins got to their beds feeling relief.

"Guys" Private started "Do you think Skippah has been planning this for a long time?"

"Why do you think so?"

"Well, Buck Rockgut told that the spy passed the information about our arrival to the enemy, whoever he meant. It sounds like they were planning this"

"I don't know Private. If so, then Skipper perhaps didn't want us to know earlier for a reason"

"Probably…" Private agreed.

"Wut is tomorow? Rico asked.

"I am afraid of what will happen to us"

"Don't worry" Kowalski said "Skipper would not let them hurt us. Maybe we will have hard training. But nothing bad will happen. I'm sure. For now I really want to get a closer look at the lab!"

"Eh' Kowalski" Rico rolled his eyes.

"Don't tell me you are not interested in the 'kaboom' room, Rico"

"Yep, kaboom!"

"Why don't we go on a little trip around the base?" Kowalski suggested, clearly excited. Normally he was the one to be in charge but when it came to science, he could not resist.

"Guys, come on. We have a ban to leave this room" Private reminded.

"Who' cares!" Rico joyed and got out of the bed, followed by Kowalski.

"I do!" Private said but he could do nothing to prevent them, they already reached the door and opened it. Unfortunately, greeted by a security guard.

"Don't even think about it" he told them and shut door before their eyes.

"Told ya" Private smiled and closed his eyes to drift into deep sleep.

Meanwhile Skipper was sitting in an office. It wasn't similar to other parts of the headquarters at all. It seemed warm, with wooden walls, floor and desk as well. Shelves filled with books, papers lying on cupboards and there was also round red carpet in the middle. Buck was sitting behind the desk.

"A spy? I thought that the security level is so high that nothing could get through it. This has always been the greatest base. How?"

"Security has lowered, you know that the situation is hard, we have sent our agents to get some information about the enemy" Buck replied.

"Who is the enemy? I am uninformed"

"We have no idea" he frowned "We do our best but that's something we have never dealt with. The enemy hid himself well, commanding his forces from the hideout. Look, We never had a spy in here, somehow this mysterious enemy managed to infect us with his people. Everybody can be an outsider now, be on your guard"

"I heard I am needed here. What is my mission?"

"You are the best agent I have ever known, if anyone could help us it would be you. I recommended you to the highest commander Tryan. You have dealt with many enemies, I believe you can take down this one as well"

"To do it, I need as many information as you got" Skipper said.

"It is classified, but you must know this" Buck said and pulled a file out of a drawer "Our embassy in Denmark found out that most of the enemy's forces are gathered there. There's an old nuclear reactor, but closed long time ago since it was too dangerous. Apparently, someone used it to run experiments there. If these experiments succeed, out enemy will obtain the most powerful weapon. We can't let that happen. We sent several agents there but only one managed to return. I fear what future will bring us…"

"Who managed to return?"

"Agent Nigel"

"Thank god he survived" Skipper breathed a sigh of relief.

"Let's get to the next thing. Your team"

"Yes, I know, I will tell them tomorrow" Skipper said and felt something he hasn't felt in a long while, was it… sadness?

"However, plans have changed" Buck informed.

"What?"

"Well, Kowalski will become one of the scientists of National Agency Lab as you wanted him to. Rico also stays in the Storm Sapper Team. But the change applies to Private. I know you wanted him to stay with Nigel and send him to our military university to train but I have orders to place him in the South Wing Agents"

"But Private is not old enough to be a part of SWA. He needs training. I know he wouldn't like it, he is not like those agents. I know what is the best for my team, and he should stay with his uncle"

"But understand, Nigel will be send on a mission because he is the only one who got so far and returned. He won't be able to stay with Private"

"But I don't allow you to place him in SWA. I am the leader of my team and I decide" The penguin flustrated.

"Skipper, you are not their leader anymore. There's no 'team' anymore" Rockgut said and lowered his head "You can't disobey the higher orders. They will be separated and Private must become an agent"

"Then I want to speak to the one who made such an idiotic decision. They will always be MY team. I am supposed to be under the command of MAAB? Fine, but I will not let you take my own high status away. And I need to see with Nigel"

"Okay, I will take you to the head of MAAB" Buck agreed and put his flipper on Skipper's shoulder "Remember, I am on your side, always"

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 **Thank you guys, I'm happy to see that someone is interested in my last story. Keep leaving the reviews and I will try to update soon :)**

 **(Sorry for my grammar mistakes, English is not my first language)**


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